鈥淎mide Resonance鈥?in the Catalysis of 1,2-伪-l-Fucosidase from Bifidobacterium bifidum

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• 作者：Jingli Liu ; Min Zheng ; Chunchun Zhang ; Dingguo Xu
• 刊名：Journal of Physical Chemistry B
• 出版年：2013
• 出版时间：September 5, 2013
• 年：2013
• 卷：117
• 期：35
• 页码：10080-10092
• 全文大小：484K
• 年卷期：v.117,no.35(September 5, 2013)
• ISSN：1520-5207

文摘

Bifidobacterium is a genus of Gram-positive bacteria, which is important in the absorption of nourishment from the human milk oligosaccharides (HMO). We present here the detailed simulation of the enzymatic hydrolysis of 2鈥?fucosyllactose catalyzed by 1,2-伪-l-fucosidase from Bifidobacterium bifidum using the combined quantum mechanical and molecular mechanical approach. Molecular dynamics simulations and free energy profiles support that the overall reaction is a stepwise mechanism. The first step is the proton transfer from N423 to D766, and the second step involves the hydrolysis reaction via the inversion mechanism catalyzed by the amide group of N423. Assisted by D766, N423 serves as the general base to activate the water molecule to attack the anomeric carbon center. E566 is the general acid to facilitate the cleavage of glycosidic bond between l-fucose and galactose units. The intrinsic resonance structure for the side chain amide group of the asparagine residue is shown to be the origin to the catalytic activity, which is also confirmed by the mutagenesis simulation of N423G.